ArticleJournal of cheminformatics2018
SPICES: a particle-based molecular structure line notation and support library for mesoscopic simulation.
Article in Journal of cheminformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
- An automated calculation pipeline for differential pair interaction energies with molecular force fields using the Tinker Molecular Modeling Package.Journal of cheminformatics · 2024Article
- Data scheme and data format for transferable force fields for molecular simulation.Scientific data · 2023Article
- Notes on molecular fragmentation and parameter settings for a dissipative particle dynamics study of a CJournal of cheminformatics · 2023Article
- MFsim-an open Java all-in-one rich-client simulation environment for mesoscopic simulation.Journal of cheminformatics · 2020Article
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Authors and funding
6 authors.
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Abstract
Simplified Particle Input ConnEction Specification (SPICES) is a particle-based molecular structure representation derived from straightforward simplifications of the atom-based SMILES line notation. It aims at supporting tedious and error-prone molecular structure definitions for particle-based mesoscopic simulation techniques like Dissipative Particle Dynamics by allowing for an interplay of different molecular encoding levels that range from topological line notations and corresponding particle-graph visualizations to 3D structures with support of their spatial mapping into a simulation box. An open Java library for SPICES structure handling and mesoscopic simulation support in combination with an open Java Graphical User Interface viewer application for visual topological inspection of SPICES definitions are provided.
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